Is PEX1 p.Ser898fs (c.2693_2705del) pathogenic?

PEX1 p.Ser898fs (c.26932705del) is classified Likely pathogenic in PEX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-21). Absent from gnomAD; Associated with Heimler syndrome 1.

What condition is associated with PEX1 p.Ser898fs (c.2693_2705del)?

PEX1 p.Ser898fs (c.2693_2705del) is associated with Heimler syndrome 1 (ClinVar).

How common is PEX1 p.Ser898fs (c.2693_2705del) in the general population?

PEX1 p.Ser898fs (c.2693_2705del) is absent from gnomAD (gnomAD).

PEX1 p.Ser898fs

c.2693_2705del · rs2484655162 · VCV3240078

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Heimler syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 16 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP 2.6, phastCons 0.99

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PEX1
Protein: p.Ser898fs
Coding: c.2693_2705del
MANE Select: NM_000466
dbSNP: rs2484655162
Type: Deletion
Location: chr7:92499717 (GRCh38)
Gene constraint: LOEUF 0.746 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.19
Residue 898: a UniProt-annotated variant site (in pbd1a)

Full PEX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Heimler syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX1 c.2072-42_2085del Likely pathogenic ★★ same condition
PEX1 p.Ala15fs Pathogenic/Likely pathogenic ★★ same condition
PEX1 p.Glu510fs Likely pathogenic ★★ same condition
PEX1 p.Gly90fs Pathogenic/Likely pathogenic ★★ same condition
PEX1 p.Ile370fs Pathogenic/Likely pathogenic ★★ same condition
PEX1 p.Leu391fs Pathogenic/Likely pathogenic ★★ same condition
PEX1 p.Thr598fs Pathogenic ★★ same condition
PEX1 p.Ser898Asn Uncertain significance ★★ ⚠ same residue

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/pex1-p-ser898fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown